HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.845 --> Intermediate <-- 0.987 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1tqha_) through the intermediate protein (d1im5a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1im5a_ Pyrazinamidase/​nicotinamidaseIsochorismatase-​like hydrolasesIsochorismatase-​like hydrolasesα/β
Hit d1tqha_ Carboxylesterasealpha/​beta-​Hydrolasesalpha/​beta-​Hydrolasesα/β

Supporting Alignments

Query <-- 0.845 --> Intermediate
DALI alignment (Z-score: 2.3 Raw score:295.90) query 1 ------------------------------------------------------------ 1 d1im5a_ 1 peealivvdmqrdfmpggalpvpegdkiipkvneyirkfkekgalivatrdwhpenhisf 60 query 1 -------------------------------------DADE-evYSALvvGLRAYVAKNG 22 :::: :::: :::::::::: d1im5a_ 61 rerggpwprhcvqntpgaefvvdlpedaviiskatepDKEAysgFEGT--DLAKILRGNG 118 query 23 FRSVLIG-lsGGIDSALVAAIACDALGaqNVYGVSMpskySSDHSKGDAAELARRTGLNF 81 ::::::: ::::::::::::::::: ::::::: :::::::::::::::::::: d1im5a_ 119 VKRVYICgvaTEYCVRATALDALKHGF--EVYLLRDavkgIKPEDEERALEEMKSRGIKI 176 query 82 RTVsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgys 141 ::: d1im5a_ 177 VQF--------------------------------------------------------- 179 query 142 tlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailel 201 d1im5a_ 180 ------------------------------------------------------------ 180 query 202 yvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnr 261 d1im5a_ 180 ------------------------------------------------------------ 180 query 262 wregh 266 d1im5a_ 180 ----- 180 FAST alignment (Normalized score: 2.15 Raw score:469.10) query 1 DADEEVYSALV------------------------------------------------- 11 d1im5a_ 1 -----------PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT 49 query 12 ----------------------------------------------------------VG 13 :: d1im5a_ 50 RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTD 109 query 14 LRAYVAKNGFRSVLIGLS----GGIDSALVAAIACDALGAQ---NVYGVSMPSKY----- 61 ::::::::::::::: :::::::::::::: ::::: d1im5a_ 110 LAKILRGNGVKRVYI---CGVATEYCVRATALDALK-----HGFEVYLL------RDAVK 155 query 62 -SSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAIS 120 ::::::::::::::::::::: d1im5a_ 156 GIKPEDEERALEEMKSRGIKIV-------------------------------------- 177 query 121 NQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTP 180 d1im5a_ 178 ------------------------------------------------------------ 178 query 181 PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYP 240 d1im5a_ 178 ------------------------------------------------------------ 178 query 241 PGTKISAKGFGKDRRLPITNRWREGH-- 266 d1im5a_ 178 --------------------------QF 179 TMalign alignment (TM-score: 0.30 Raw score:81.01) query 1 --------------DADE------EVYSALVVGLRAYVAKN-G-FRSVLIGLSGG----- 33 ::: ::: ::::::::::::: : ::::::::::: d1im5a_ 1 PEEALIVVDMQRDF-MPGGALPVPEGD-KIIPKVNEYIRKFKEKGALIVATRDWHPENHI 58 query 34 -----------ID-SA---LVAAIACDALGAQNVYGVSMPSKYSSDHSK---GDAAELAR 75 :: : :::::: ::: :::::::: :::::: d1im5a_ 59 SFRERGGPWPRHCV-QNTPGAEFVV--DLP-EDAVIISK----ATEPDKEAY-------- 102 query 76 RTGLNFRTVSIEPMFDAYMASLGLTGLAEEN-LQSRLRGTTLMAISNQ--EGHIVLAPGN 132 : ::::::::::::::: ::::::: d1im5a_ 103 ------------------------------SG-FEGTDLAKILRGNGVKR---VYICGVA 128 query 133 KSELAVGYSTLYGDS---V-GAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASIT 188 :::: ::::::::: : ::::::::::: d1im5a_ 129 TEYC--VRATALDALKHGFEVYLLRDAVKGI----------------------------- 157 query 189 KPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 248 :: :: :: : :::::::: ::::::: d1im5a_ 158 -------KP-ED-EE----------------------R-ALEEMKSR-GIKIVQF----- 179 query 249 GFGKDRRLPITNRWREGH 266 d1im5a_ 180 ------------------ 180 HHsearch alignment (Probability: 0.10 E-value:0.05) query 13 GLRAYVAKNGFRSVLIGL---SGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGD 69 :::::::::::::::::: ::::::::::::: :::: :::::::::::::::::: d1im5a_ 109 DLAKILRGNGVKRVYICGVATEYCVRATALDALK---HGFE-VYLLRDAVKGIKPEDEER 164 query 70 AAELARRTGLN 80 ::::::::::: d1im5a_ 165 ALEEMKSRGIK 175
Intermediate <-- 0.987 --> Hit
DALI alignment (Z-score: 3.9 Raw score:437.90) d1im5a_ 1 ---------PEEALIVVDMQRDfmpggalpvpegdkiipkVNEYIRKFKEKGALIVATRD 51 ::::::::::::: :::::::::::::::::::: d1tqha_ 1 ppkpfffeaGERAVLLLHGFTG--------------nsadVRMLGRFLESKGYTCHAPIY 46 d1im5a_ 52 WHpenhisfrerggpwprhCVQNTpgaefvvdlpedaviiskatePDKEA---YSGFegT 108 :: ::::: ::::: :::: : d1tqha_ 47 KG-----------------HGVPP------------------eelVHTGPddwWQDV--M 69 d1im5a_ 109 DLAKILRGNGVKRVYICGVAteYCVRATALDALKHGFeVYLLrdaVKGI----------- 157 :::::::::::::::::::: ::::::::::::::: :::: :::: d1tqha_ 70 NGYEFLKNKGYEKIAVAGLS--LGGVFSLKLGYTVPI-EGIV--tMCAPmyikseetmye 124 d1im5a_ 158 ------------------------------------------------------------ 158 d1tqha_ 125 gvleyareykkregkseeqieqemekfkqtpmktlkalqeliadvrdhldliyaptfvvq 184 d1im5a_ 158 -------KPEDEERALEEmKSRG-----------------------ikIVQF------- 179 ::::::::::: :::: :::: d1tqha_ 185 arhdemiNPDSANIIYNE-IESPvkqikwyeqsghvitldqekdqlheDIYAflesldw 242 FAST alignment (Normalized score: 2.92 Raw score:607.00) d1im5a_ 1 P----------EEALIVVDMQRDFMPGGALPVPEGDK------IIPKVNEYIRKFKEKGA 44 :::::: ::::::::::::::::: d1tqha_ 1 -PPKPFFFEAGERAVLL--------------------LHGFTGNSADVRMLGRFLESKGY 39 d1im5a_ 45 LIVATRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSG 104 ::::: d1tqha_ 40 TCHAP------------------------------------------------------- 44 d1im5a_ 105 FEG------------------------TDLAKILRGNGVKRVYICGVAT--EYCVRATAL 138 :::::::::::::::::: ::::::::: d1tqha_ 45 ---IYKGHGVPPEELVHTGPDDWWQDVMNGYEFLKNKGYEKIAVA----GLSLGGVFSLK 97 d1im5a_ 139 DALKHGF-EVYLLRDAVKGI---------------------------------------- 157 ::::::: :::: d1tqha_ 98 LGYTVPIEGIVT--------MCAPMYIKSEETMYEGVLEYAREYKKREGKSEEQIEQEME 149 d1im5a_ 158 --------KPEDEERALEEMKSRGIKIVQF------------------------------ 179 :::::::::::::: d1tqha_ 150 KFKQTPMKTLKALQELIADVRD--------HLDLIYAPTFVVQARHDEMINPDSANIIYN 201 d1im5a_ 180 ----------------------------------------- 180 d1tqha_ 202 EIESPVKQIKWYEQSGHVITLDQEKDQLHEDIYAFLESLDW 242 TMalign alignment (TM-score: 0.35 Raw score:62.67) d1im5a_ 1 -------------PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVN-E----YIRK---- 38 ::::::: ::: ::::::::: : :::: d1tqha_ 1 PPKPFFFEAGERA----VLLLHGF-TGN---------SADVRMLGRFLESKGYTCHAPIY 46 d1im5a_ 39 ----------------------------FK----EKGALIVA--TR-D------------ 51 : :::::::: :: : d1tqha_ 47 KGHGVPPEELVHTGPDDWWQDVMNGYEF-LKNKGYEKIAVAGLSLGGVFSLKLGYTVPIE 105 d1im5a_ 52 ------------WHPENHISFRERGGPWPRHCV--QNTPG-------------------- 77 :::::: : :::::: : d1tqha_ 106 GIVTMCAPMYIK----SEETMY---E-GVLEYARE----YKKREGKSEEQIEQEMEKFKQ 153 d1im5a_ 78 ----AEFVVDLPEDAVIISKATEPDKEAYSGFEGTDLAKILRGNGVKRVYICGVATE-YC 132 :::: ::: : ::::::: :::::: :::::::::: :: d1tqha_ 154 TPMK----------------TLKA-LQE--L-IADVRDH-LDLIYA-PTFVVQARHDEMI 191 d1im5a_ 133 VRATALDALKHG-F--EVYLLR-DAVKGIKP--EDEERAL-----EEMKSRGIKIVQF-- 179 :::::::::::: : :::::: :::::: :: : :::: d1tqha_ 192 NPDSANIIYNEIESPVKQIKWYE--QSGHVITL--DQ--EKDQLH---------EDIYAF 236 d1im5a_ 180 ------ 180 d1tqha_ 237 LESLDW 242 HHsearch alignment (Probability: 0.06 E-value:0.07) d1im5a_ 108 TDLAKILRGNGVKRVYICGVATEYCVRATALDALKH----GFEVYLLRDAVK 155 :::::::::::::::::::::::::::::::::::: :::::::::::: d1tqha_ 167 ADVRDHLDLIYAPTFVVQARHDEMINPDSANIIYNEIESPVKQIKWYEQSGH 218